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M. Alizadeh, J.Z. Li, H. Choi, R.M. Myers, D. Yasumura, M.T. Matthes, M.M. LaVail, D. Vollrath; Diurnal Gene Expression in Retinal Pigment Epithelium . Invest. Ophthalmol. Vis. Sci. 2005;46(13):3994.
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Purpose:Many mammalian peripheral tissues such as liver, heart, and kidney have circadian clocks that generate transcriptional rhythms that are important for the daily timing of physiological processes. For example, photoreceptor outer segments are shed in a circadian fashion. In light–entrained rats and mice, a burst of rod disc shedding and RPE phagocytosis occurs soon after lights on. Here we report circadian gene expression changes in mouse retinal pigment epithelium samples isolated at different points in the circadian cycle. Methods:Mice were raised to approximately 2 months of age and entrained to a 12–hr light/dark cycle for ≥2 weeks. RPE/choroids/sclera tissues were collected over three consecutive cycles at t=0.5, 1, 1.5, 4, 11, 13, 16, and 23 hrs, for a total of 24 time points. RNA samples were extracted from dissected RPE/choroids/sclera, labeled, and hybridized in a two–color format to spotted cDNA microarrays containing 42,000 mouse cDNA clones representing 25,000–30,000 unique. We applied standard time–series frequency domain analysis and used the Fisher’s g statistics to identify periodically expressed genes (Wichert et al Bioinformatics 2004 20: 5–20). Results:We found that up to 4% of genes in RPE/choroid are diurnally expressed. Several genes, such as Bmal1, Nr1d2, and Tef, were found in previous studies as diurnal genes in peripheral tissues such as liver and heart. However, a majority of the RPE diurnal genes do not overlap with those in other tissues. Conclusions:Our results indicate that only a small number of core circadian genes carry out general regulation across diverse peripheral tissues, and a majority of the circadian regulated genes in RPE/choroid are tissue specific. Global expression profiles of these genes therefore reflect diverse processes in the RPE and may shed new light on transcriptional rhythms and pathways that regulate diurnal patterns such as OS disc shedding and RPE phagocytosis.
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